Move vec.h to math/

Most of the changes are scripted replacement of include paths.
Exceptions:
- #includes in the moved file were cleaned up slightly, and include
  guards adjusted.
- Places where it was included as "gromacs/legacyheaders/vec.h" were
  handled manually and the include order adjusted.
- Removal of unnecessary #include "vec.h" from update.h revealed some
  transitive dependencies that were fixed.  Some associated include
  order cleanup in these files.
- Removed some duplicate includes.
- Remove dependency from linearalgebra/matrix.c to vec.h (only needed
  for a single sqr()) to avoid a cyclic math <-> linearalgebra
  dependency.

Part of #1415.

Change-Id: I7ece6eafa22139215510148807c5979f8950a885